Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Lmnb1

Cell type

Cell type Class
Liver
Cell type
Liver
MeSH Description
A large lobed glandular organ in the abdomen of vertebrates that is responsible for detoxification, metabolism, synthesis and storage of various substances.

Attributes by original data submitter

Sample

source_name
Liver
tissue
liver
genotype
WT
age
4 months
diet
Western, 8 wks
chip antibody
Lamin B1

Sequenced DNA Library

library_name
GSM5916360
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
[RNA-Seq] Liver RNA was isolated from mice on control and Western diet (8 weeks and 12 weeks). Quality of RNA samples was analyzed using Agilent RNA 6000 Nano Kit (Bioanalyzer, Agilent Technologies). Samples with RIN scores above 9.5 were used in library preparation. 1 µg of total RNA was used to isolate mRNA (NebNext Poly(A) mRNA Magnetic Isolation Module). [RNA-Seq] Libraries of resulting mRNA were prepared using NebNext Ultra II RNA library preparation kit. All samples were sequenced on Illumina NextSeq 500. [ChIP-Seq] Snap-frozen liver (100 mg) from mice on normal and Western diet (8 weeks and 12 weeks) or from normal and NAFLD patients was used to prepare chromatin. Foxa2‐specific rabbit antiserum (Seven Hills Bioreagents, WRAB‐1,200) and rabbit antibody to lamin B1 (Abcam, Ab16048) were used for immunoprecipitation. [ChIP-Seq] Libraries were prepared according to Illumina's instructions. Briefly, DNAs were blunted with a combination of T4 DNA polymerase, Klenow polymerase, and T4 PNK, then a single 3′-end “A” base was added using Klenow exo (3′-to-5′ exo minus). Multiplex adapters were then ligated to the ends of the modified DNA. After adapter ligation DNA was PCR amplified with Broad custom primers for 16 cycles and library fragments of ~280 bp (~150-bp insert plus ~130-bp adaptor and PCR primer sequences) were isolated using Pippin Prep agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. All libraries were sequenced on Illumina NextSeq 500.

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
49106532
Reads aligned (%)
63.9
Duplicates removed (%)
23.0
Number of peaks
474 (qval < 1E-05)

mm9

Number of total reads
49106532
Reads aligned (%)
63.8
Duplicates removed (%)
23.1
Number of peaks
449 (qval < 1E-05)

Base call quality data from DBCLS SRA